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OBI consortium

Quick Term Template: Class addition by design patterns Full tutorial available at : http://obi- ontology.org /page/ Quick_Term_Templates. OBI consortium. Philippe Rocca-Serra proccaserra @gmail.com http:// www.isa-tools.org. Carlo Torniai torniai@ohsu.edu. Background. Problem:

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OBI consortium

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  1. Quick Term Template: Class addition by design patternsFull tutorial available at:http://obi-ontology.org/page/Quick_Term_Templates OBI consortium Philippe Rocca-Serra proccaserra@gmail.com http://www.isa-tools.org Carlo Torniai torniai@ohsu.edu

  2. Background • Problem: How to enable knowledge experts to add large number of classes with as little hassle as possible? • Batch processing capability • Automatic class axiomization • Identification of recurring patterns in knowledge representation

  3. Tools & Prerequisites • Protégé 3.4.4 • Mapping Master Plugin (O’Connor et al, 2010) [http://protege.cim3.net/cgi-bin/wiki.pl?MappingMaster] • An OWL Ontology • Knowledge of OWL Manchester Syntax • A use case, a pattern/formal representation!

  4. QTT approach overview Processing the Spreadsheet with Mapping Master

  5. Principle: 1. Finding a pattern • Measuring concentration of glucose in urine • Measuring concentration of calcium in plasma • Measuring concentration of CO2 in air • Measuring concentration of PSA in plasma • …….

  6. Principle: 2.modeling step • Measuring concentration of glucose in urine • Measuring concentration of calcium in plasma • Measuring concentration of CO2 in air • Measuring concentration of PSA in plasma • <data> <quality> <evaluant> <analyte>

  7. QTT example • Target Ontology: OBI.owl • Constraints: • Map terms (or submit if not available) to compatible ontologies (i.e. sharing the same top level ontology, here BFO 1.1) • Import those terms External.owl + ExternalDerived.owl files

  8. Principle: 3. Class Definition and formalization

  9. Principle: 4.Process with Mapping Master

  10. Device example Class: @A*(rdfs:label) SubClassOf: @B*(rdfs:label), has_function some @C*(rdfs:label), has_function some @D*(rdfs:label),

  11. Future Work • Automatic Import via MIREOT mechanism of external and externalDerived.owl files (or equivalent structure) in target ontology during QTT processing • Creation of a library of QTT available from OBI • Analyte template • Service template • Instrument template • Single nucleotide mapping structure assay More if people willing to share!

  12. Reference / Acknowledgements Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates P. Rocca-Serra, A. Ruttenberg, M. J. O'Connor, T. Whetzel, D. Schober, J. Greenbaum, M. Courtot, S. A. Sansone, R. Scheurmann, B. Peters ( & OBI consortium) Journal of Applied Ontology, 6, 13-22. Published in 2011 TUTORIAL: http://obi-ontology.org/w/images/d/dd/Howto-QTT-Template-Import-MappingMaster.doc

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